


It's Us Against the Universe

by CuteRubberBoat



Category: Star Trek: Alternate Original Series (Movies)
Genre: Always-a-girl Kirk, F/M, Genderbending, Genderswap, Post-Star Trek: Into Darkness, Unplanned Pregnancy
Language: English
Status: In-Progress
Published: 2013-09-25
Updated: 2013-09-25
Packaged: 2017-12-27 14:01:50
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,856
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/979780
Author URL: https://archiveofourown.org/users/CuteRubberBoat/pseuds/CuteRubberBoat
Summary: <blockquote class="userstuff">
              <p>Jamie Kirk and Leonard McCoy have been friends for a long time, but there are these other feelings they had never acted on – until they do. Their timing is wrong, of course, and they have to deal with an unplanned pregnancy after a one-night stand. Post-Khan.</p>
            </blockquote>





	It's Us Against the Universe

**Author's Note:**

> I'm writing this for the STID Kink Meme at Livejournal, filling the request of Always-A-Girl-Kirk and McCoy dealing with pregnancy as the result of a one-night stand and realizing they love each other. English isn’t my first language, but [Noo](http://archiveofourown.org/users/noo/works) was kind enough to beta-read this piece. Any mistakes still around are on me, since I keep changing things. 
> 
> Per OP’s request at LJ, imagine that Jamie Kirk looks like Jennifer Morrison, but with Chris Pine's blue eyes.

 

Where Jamie T. Kirk was concerned, where it mattered to her the most, it was almost the same after Khan. Almost being the key word there.

She still had the Enterprise. _Brand new and already broken and fixed twice._

She still had her crew. _Not all of them._

She still had Bones. _She never had him_.

At least that is what the Captain told herself when she needed some sort of reassurance that there was a purpose in all the carnage unleashed in the past months – that nothing had changed much. So many lives lost had to mean something, even her own, although it was the impact of Jamie’s death on others that had affected her the most. Being dead mattered the less for her. Being back was a different story.

Physically, after being poked, prodded, probed, and her body submitted to every single test available, it had been established that Jamie was still Jamie. The serum her Chief Medical Officer had developed – that small miracle Leonard H. McCoy had pulled off to save her life – hadn’t affected the Captain’s genes. Extensive exams had determined that there had been no change in her genetic material. Not a trace of the murderous lunatic who had killed thousands. It had been a relief to Jamie, though she didn’t voice it, that she was the same. No super strength, no super intellect, no super powers of any sort. She was still allergic to a few toxoids. Her bright blue eyes still suffered from dryness from time to time. Her body still carried a couple of scars from a past very few had known about.

Emotionally…well, as far as her heart, mind and soul went, it had been a different story. Khan _did_ leave a mark on her. The eminent destruction of the _Enterprise_ and its crew had pushed Jamie to the edge and she hadn’t wavered. She did take the jump, figuratively and literally, never a choice, never a doubt.  Dying wasn’t as painful as she imagined. It was scary, but not despairing, and the amount of sadness she had felt made her ache more than the radiation poisoning her cells. The taste in her mouth was bittersweet, of what she had attained and what she would not accomplish.

To never boldly go to the galaxies and worlds that waited for her. _The universe was her home._

To never sit on the chair again. _It was made for her._

To never be with the family she had just found another time. _These were her sisters and brothers._

To lose Bones forever. _He couldn’t leave you behind._

They say mistakes are how you learn, and it had been a hard lesson for Jamie to witness the effect of her death – or near death experience, depending on who was privy to the real truth. She had believed that her loyalty toward her crew was greater than her crew’s loyalty to her, and if Christopher Pike had been alive he would have knocked her off of her pedestal for the lack of humility – to think she was the better person there and had more to offer to them than the other way around was a twisted way of arrogance covered by the excuse of altruism.

It had been a very humbling experience to be the receiver of the several degrees of affection displayed by her crew. It had crushed her spirit to see how they had mourned her, and it had warmed her whole being to learn they considered her more than just their Captain. They genuinely cherished her. She had sought love and acceptance all her life, and it had taken her nothing less than dying to see that she already had that.

Though, if she, Jamie, was honest with herself, she knew she had been accepted, loved and cherished long before setting foot on the _Enterprise_.

_Damnit, Jim._

Even if she had dealt with this exactly like she did with other issues in her life – deny, pretend they never existed, bury them six feet under with all the other ghosts, dead or alive, never really forgetting or forgiving. _Father. 800 people in 12 seconds. Frank. Tarsus. Sam. Mother. Vulcan. Pike. Tarsus._

For someone who craved love – real love - so much, it was unsettling to deal with the amount of fondness she received. They offered it to her for free, smiles and bright eyes, and Jamie felt her throat tighten when any of them came by.  To the vast majority of the _Enterprise_ crew – and the rest of the world – the Captain being alive had nothing to do with Khan, but with her CMO being able to reverse the degradation caused to her cells by acute radiation syndrome using groundbreaking science that nobody had ever done before. That, combined with Bones’ unique understanding of Jamie’s physiology, made for a win. Beating death was not that easy, but the elaborated explanation about brain activity, organs’ life span and emulation of heart functions reasoned even among the skeptical – she never died, she hadn’t been dead, that was the official tale. For all it was worth, Jamie still didn’t know if their faith in the medical and science team was really that strong or if, to them, it was just simpler that way and all in all a well told half-truth really goes a long way. Especially when there is Starfleet erasing any trace of the augments as much as possible, and succeeding.

Had Jamie not seen all debriefs and hearings, debrief after debrief, hearing after hearing, maybe then she would have felt bad for lying – no, not lying, omitting. But she had watched and re-watched every single one of them, and those unaware of the role the genetically-engineered criminal had played in the captain’s death and re-birth had no idea of what they had been spared from. Some had attended more than one meeting, like Spock, Scotty and Carol Marcus, the three of them too entangled in the mess left by a maniac augment and a corrupt admiral. Jamie still cringed at the way Scotty’s face fell when asked what kind of Engineering was that in the _Enterprise_ that it was so easy for anyone to enter the death trap called warp core room, or how Carol was a mix of rage and shame whenever the word ‘father’ was mentioned – even the almost imperceptible twist of Spock’s mouth spoke loud and clear about the pressure they had been put through, none of them cracking, at least publicly. What they did in the privacy of their homes was another story – although Sulu’s amazing  rowhouse, a family heritage, and Uhura and Spock’s building had been swept by the _Vengeance_ , and Jamie never had the courage to ask where they had slept those first days back on Earth.

Medals and promotions and praises would never make up for the loss, but their official records would tell a tale of bravery and brilliancy in face of danger and death.

Not all records, of course.

There was the matter of Starfleet Medical Command tearing Bones apart in what had been one of the most brutal debriefings Starfleet had ever witnessed – a court-martial was more like it -, each one of the brass appalled and insulted that the doctor had had the audacity to even consider cheating death. That he had actually succeeded in coming up with a way to bring back his Captain to life scared and awed and enraged Bones’ peers in equal measure, Jamie was sure. It had been one of the most notable achievements in the medical field in ages, and also one of the most terrifying acts ever performed by someone who was supposed to honor an oath forged with words and moral principles never to be taken with less than the uttermost respect.

A doctor did no harm, for life was not his to take.

It was not his to give, either.

Bones had been summoned by the Surgeon General, but by the fury on some of the commanders’ faces one could readily believe the CMO had conjured the wrath of God Himself, angels of mercy ready to avenge all the medical ethics he had lived by until Khan and then ignored repeatedly after Khan. Question after question, they had harassed him endlessly about the events from the moment _Enterprise_ had encountered the augment to the night when Jamie had opened her eyes.  Each answer the doctor gave his superiors raised a new set of questions, his face impassible and neutral the whole time, ‘no’ and ‘yes’ and well-mannered declarations that weren’t fooling anyone. They all knew too well that his eyes were saying what his heart truly felt – _fuck it all, I regret nothing_.

Jamie was still in the hospital during the hearing, and she hadn’t known about it until two days later when she eavesdropped on Spock and Uhura talking about the rumors of the debriefing being a-not-so-concealed trial and the doctor’s medical license being permanently revoked as soon as the captain was officially cleared for duty. That piece of information had sent Jamie into an outburst of indignation and she had almost knocked the other woman over in her urge to get up. Her First Officer had to pin her shoulders down on her bed with a vice-like grip, while Uhura patiently explained that there was nothing the captain could do, because the big wigs at Starfleet Medical were not listening to Starfleet Military on the subject. The connections Jamie and Spock had in the Admiralty and whatever leverage she had gained after saving Earth meant almost nothing for the very corporative-tight medical field. Spock had already worked on a complicated equation that predicted the odds of Bones being punished at 100 percent, but the probability of losing his license for good a ‘mere’ 58.8 percent. The likelihood of the doctor being discharged from Starfleet was 73.9 percent, though, and Jamie lacked the courage to ask the  odds at having her CMO back on the _Enterpris_ e – would they allow him anywhere near the flagship? _Near her? Would he want that?_

That Bones had been suspended from practicing on Earth for the time being but was still allowed to practice in space, well, this, Jamie had learned later, was the middle ground sanction reached by opposite sides at Starfleet Medical Command.  In theory, it almost seemed fair. But the Surgeon General would not hold the position without knowing how to twist the scalpel – and every single man, woman or alien in the medical track knew that Philip Boyce held that blade with the experience and expertise of a man who had the job by merit and not by political schemes.

It was for the best that the five years mission was still on, because Jamie was sure, she was sure had he stayed on the planet, that Bones would have broken whatever agreement he had been forced to sign at the first sight of a sprained ankle or a suspicious cough - heck, a less than fully rested face would do the trick. Leonard McCoy was a doctor first and foremost and no military ruling could ever bend, break or ban the healer in him.

Knowing Bones, how he didn’t mince words and wore his heart in his sleeve all the time, Jamie had to wonder how much it was costing him to not lash out at her for basically committing suicide. Putting her life on the line came with the job, but entering a radioactive chamber was, by all accounts, supreme idiocy. As Scotty had pointed out later, much later, there were radiation suits in a locker with a big red sign and plexiglass doors just outside the room, and Chekov had excitedly explained the vests would have reduced contamination greatly making her treatment easier. What made them believe for a second that there had been time for suits and preventive measures would always be beyond her. Still, it hadn’t changed the fact she had aligned the warp core with her feet, that her body had been bathed in enough Gamma rays to kill an army, that she had died, that Bones had not been there because no one, _no one_ , not even Jamie herself, had called him, and, yet, her CMO – her friend – had unceremoniously dismissed all her attempts to talk about what had happened.

_“Bones…”_

_“You don’t get to ‘Bones’ me about any of that.”_

The epic fight Jamie had been expecting and braced herself for never happened. Her stay at the hospital, 38 long excruciating days, had been filled up with her own debrief, administrative crap, visits, resting and a series of sessions of hell in the form of physical therapy for her joints, all sore and hard and cracking loud when she tried to move. Bones had been at her side every painful step through it – fall, get up, fall, get up, fall, get up –, always present when he wasn’t being hassled by a superior who – Jamie was sure – had not dealt in ages with the urgent decisions made in a sickbay deep into space. He had been allowed to treat her until her she was officially released, the suspension of his license taking effect immediately after that, while M’Benga, who was already helping Bones and with Boyce getting daily updates, took over as her doctor, following the rest of her recovery – or whatever they called being regenerated from the inside.

Years later, three things would always stick when Jamie remembered these final days in the hospital: how young Chekov had been, the smell of M’Benga’s cologne, sweet, spicy and slightly headache inducing, and the way Bones’ jaw shut so tight that she could almost hear his teeth gritting, tension making his whole body so taut it looked like he would – and should – snap at any moment. He was bound to crack, they were all bound to break apart sooner or later, what with the several levels of depression they were all battling. Back then, the captain had been pretty suspicious that Bones’ breaking pointing had  occurred sometime during that month off he took in Georgia after she was released, because he was a much less strained man when he came back. But he had lost weight, too, and his eyes carried a deep new sorry, in a way that screamed that the universe had found a fresh way to beat the living shit out of him, and the captain was wise enough to not try to dig it out of him.

Jamie herself had the mother of all meltdowns the night she is in her kitchen, grabbing something for a late snack, even if she isn’t eating much these days. The lights flicker, the minor earthquake shakes the ground just a little, she blinks and, suddenly, the captain is back at the _Vengeance_ bridge, and she tries, God, she tries to stop the memories, but it comes with the force a of rail crash, Pike’s lifeless eyes, Khan’s bare hands on Marcus’ skull, his boot on the admiral daughter’s leg, and it is not Carol’s or Spock’s screams anymore, it is Jamie’s own voice – _shut up, shut up, shut up_ – piercing her ears while the sobs come one after another, non stop, never stopping, will they ever stop, won’t stop, she can’t stop, and when the sun rises in the morning she is still lying on the cool tiles of the floor, arms around her torso, face buried on her chest, her whole body more battered than it ever was in the warp core room.

During the mandatory psychiatric sessions, they say it was the five seconds power outage that trigged the flashbacks, and Jamie plays her part, fake-agreeing after some calculated reluctance, because how can she tell them that it was the unsteady ground, when her job is to command a starship where she can feel the constant humming of the engines vibrating under her feet almost everywhere? The psych brigade is good, but dropping famine and a nutcase dictator on Jamie’s lap in order to make her to talk will not prevent her from getting the only three words she wants from them – _fit for duty_.

As contradictory as it looked, going back to space had been a clean slate for almost all of them. San Francisco was a city scarred by destruction, large areas still devastated or under reconstruction. The very few places that had been rebuilt had that brand-new aspect that told a story no one wanted to relive. It didn’t help that the _Vengeance_ had erased Alcatraz from the horizon or that pieces of the ship were still embedded in the bay. Restoration couldn’t be as fast as they all wished it to be, and it would never bring back the post-card San Francisco landscape exactly as they remembered.

Nothing would be exactly as they remembered.

Assembling the crew for their great voyage had been a very complicated puzzle. Several captains had requested crew members from the _Enterprise_ for their ships, vessels from all sizes and for all functions, old and new, some that were being put together when Nero destroyed Vulcan, others that had been built after Narada. There were people who had volunteered to go, there were people who were with Jamie during Nero and Khan that had chosen to not go – because they had had enough, because five years is a lifetime, because there are great things they can do on Earth, because there are family and friends, because it is solid ground and real food and hot water and an infinite supply of fresh air, and who can really blame them?

Scotty and Uhura had been a done deal since the beginning, because the fleet’s command would never let the flagship enter deep space for five years without their best engineer – and he is the best, even if there is a certain Beagle officially still missing – and a communications officer that is proficient in almost every language and dialects known to date. Spock is wanted by three different ships and New Vulcan, but he settles for Uhura and Jamie, and the captain gets Sulu and Chekov and Janice. She also gets more experienced people; officers easily twice her age and ten times more used to space than her or any other cadet that boarded the _Enterprise_ in her first voyage; people who are accustomed to work and live confined for long periods of time, who have seen much and who wanted to see even more. Some are geniuses, some are hard-working military. Some are human, some are not. Jamie battles for a bunch, loses a few, and is relieved – _relieved_ \- when Boyce orders Bones to the _Enterprise_ , despite the fact that every single war vessel captain in the fleet had eyes on the doctor. Bones picks up M’Benga and brings Chapel back, and Jamie doesn’t dare to protest.

It had taken a little less than one year to fix the _Enterprise_ , and with the ship out of commission, the crew had taught, worked, studied and helped wherever they could. It had not been enough time to heal all the injuries or erase all the tension, but at their farewell party, watching the men and women that were willing to put their lives in her hands, Jamie had realized that it had been sufficient to mourn and grieve and lick their collective and individual wounds and rise and move forward while preparing for space, the final frontier, right there, right after the next nebula, waiting for them with the stars.

Their mission… Oh, it was exciting, it was new, it was an adventure, it was a blast, and Jamie felt alive. _Alive_. It was everything she had always wanted, always dreamt of. It was much more than that.

Until the _Enterprise_ literally stumbled over a Klingon ship after warp jumping into some supposedly peaceful galaxy. The loss had been great, and if half of the injured didn’t join the dead in the morgue that was because the captain had one of the best, probably the finest surgeon in the entire fleet as her CMO – even though she knew that for Leonard McCoy one single death was the ultimate defeat, and there had been, Jesus, so many more losses.

But she was the Captain and she counted every small victory and small mercy, and when Bones finally succumbed to a hypo ministered by M’Benga, almost three days after they were first hit, deep exhaustion and grief and loss marked on his face, his body curled on the couch in his office, Jamie left a bottle of the richest whiskey Scotty had on the doctor's desk. She also left a soft kiss on Bones' right cheek, the stubble of his unshaven face sending little shocks to her lips. Before she turned around, she took a moment to look at the mouth she had been so close to kissing a million times, the tiny little freckles on his skin that had no place in a man that had spent the majority of his adult life locked in surgical wings and labs, the strong eyebrows that, for once, were not furrowed.

Bones.

 _Her_ Bones. 

Except he wasn't hers, and would never be, if Jamie had any say in that matter, because she was not going to not have Bones in her life and giving in to that attraction – really, who wouldn't be attracted to him – and those feelings – she wasn't going to delve into these – was the fastest way to fuck up the best friendship she ever had, the first true friendship she had ever known.

So Jamie did what she did the best. She had an earful from the Admiralty, reassembled her crew and ship and headed home, so the _Enterprise_ could be properly fixed again – six months at least, Scotty had said. It was not how the captain had envisioned her trip back, but she had learned when to pick her battles and having beaten Klingons was the guarantee that the mission was still on with herself commanding the bridge. 

It was with that certainty and with the confidence she possessed in spades that Jamie entered the noisiest bar on a small second class planet just two weeks distant to Earth. The kind of place where people got drunk, got high, got into fights and got fucked, all the four in the same night if they were lucky, but the captain was more than happy with the usual trifecta – alcohol, punches in a safe boxing ring and sex.

The first, she got from the cute humanoid behind the counter, a Syrion with black eyes who gave Jamie a lascivious once over, two bottles of the strongest Romulan ale in the house and the door code for the supply room in the back.  
  
The second, she actually got right on the face from a very tall brunette that later Jamie would learn was the ex of the gorgeous – and sassy - redhead with whom Bones left the bar.

The third, Jamie got from Lee Hirada, the captain of the _U.S.S. Yamato Mistral_ , who happened to be the father of her child.

Or, at least, the biological father.

**Author's Note:**

> Reviews are love. Hate it, love it, just let me know, and thank you very much for reading.


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